2026-04-16 22:38:20 +02:00
<!doctype html>
< html lang = "en" class = "no-js" >
< head >
< meta charset = "utf-8" >
< meta name = "viewport" content = "width=device-width,initial-scale=1" >
< link rel = "prev" href = "../storage/" >
2026-04-29 22:52:42 +02:00
< link rel = "next" href = "../unitig_evidence/" >
2026-04-16 22:38:20 +02:00
< link rel = "icon" href = "../../assets/images/favicon.png" >
< meta name = "generator" content = "mkdocs-1.6.1, mkdocs-material-9.7.6" >
< title > MPHF selection - obikmer< / title >
< link rel = "stylesheet" href = "../../assets/stylesheets/main.484c7ddc.min.css" >
< link rel = "preconnect" href = "https://fonts.gstatic.com" crossorigin >
< link rel = "stylesheet" href = "https://fonts.googleapis.com/css?family=Roboto:300,300i,400,400i,700,700i%7CRoboto+Mono:400,400i,700,700i&display=fallback" >
< style > : root { --md-text-font : "Roboto" ; --md-code-font : "Roboto Mono" } < / style >
< script > _ _md _scope = new URL ( "../.." , location ) , _ _md _hash = e => [ ... e ] . reduce ( ( ( e , _ ) => ( e << 5 ) - e + _ . charCodeAt ( 0 ) ) , 0 ) , _ _md _get = ( e , _ = localStorage , t = _ _md _scope ) => JSON . parse ( _ . getItem ( t . pathname + "." + e ) ) , _ _md _set = ( e , _ , t = localStorage , a = _ _md _scope ) => { try { t . setItem ( a . pathname + "." + e , JSON . stringify ( _ ) ) } catch ( e ) { } } < / script >
< / head >
< body dir = "ltr" >
< input class = "md-toggle" data-md-toggle = "drawer" type = "checkbox" id = "__drawer" autocomplete = "off" >
< input class = "md-toggle" data-md-toggle = "search" type = "checkbox" id = "__search" autocomplete = "off" >
< label class = "md-overlay" for = "__drawer" > < / label >
< div data-md-component = "skip" >
2026-04-29 22:52:42 +02:00
< a href = "#mphf-selection-two-phase-indexing-architecture" class = "md-skip" >
2026-04-16 22:38:20 +02:00
Skip to content
< / a >
< / div >
< div data-md-component = "announce" >
< / div >
< header class = "md-header md-header--shadow" data-md-component = "header" >
< nav class = "md-header__inner md-grid" aria-label = "Header" >
< a href = "../.." title = "obikmer" class = "md-header__button md-logo" aria-label = "obikmer" data-md-component = "logo" >
< svg xmlns = "http://www.w3.org/2000/svg" viewBox = "0 0 24 24" > < path d = "M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54" / > < / svg >
< / a >
< label class = "md-header__button md-icon" for = "__drawer" >
< svg xmlns = "http://www.w3.org/2000/svg" viewBox = "0 0 24 24" > < path d = "M3 6h18v2H3zm0 5h18v2H3zm0 5h18v2H3z" / > < / svg >
< / label >
< div class = "md-header__title" data-md-component = "header-title" >
< div class = "md-header__ellipsis" >
< div class = "md-header__topic" >
< span class = "md-ellipsis" >
obikmer
< / span >
< / div >
< div class = "md-header__topic" data-md-component = "header-topic" >
< span class = "md-ellipsis" >
MPHF selection
< / span >
< / div >
< / div >
< / div >
< script > var palette = _ _md _get ( "__palette" ) ; if ( palette && palette . color ) { if ( "(prefers-color-scheme)" === palette . color . media ) { var media = matchMedia ( "(prefers-color-scheme: light)" ) , input = document . querySelector ( media . matches ? "[data-md-color-media='(prefers-color-scheme: light)']" : "[data-md-color-media='(prefers-color-scheme: dark)']" ) ; palette . color . media = input . getAttribute ( "data-md-color-media" ) , palette . color . scheme = input . getAttribute ( "data-md-color-scheme" ) , palette . color . primary = input . getAttribute ( "data-md-color-primary" ) , palette . color . accent = input . getAttribute ( "data-md-color-accent" ) } for ( var [ key , value ] of Object . entries ( palette . color ) ) document . body . setAttribute ( "data-md-color-" + key , value ) } < / script >
< / nav >
< / header >
< div class = "md-container" data-md-component = "container" >
< main class = "md-main" data-md-component = "main" >
< div class = "md-main__inner md-grid" >
< div class = "md-sidebar md-sidebar--primary" data-md-component = "sidebar" data-md-type = "navigation" >
< div class = "md-sidebar__scrollwrap" >
< div class = "md-sidebar__inner" >
< nav class = "md-nav md-nav--primary" aria-label = "Navigation" data-md-level = "0" >
< label class = "md-nav__title" for = "__drawer" >
< a href = "../.." title = "obikmer" class = "md-nav__button md-logo" aria-label = "obikmer" data-md-component = "logo" >
< svg xmlns = "http://www.w3.org/2000/svg" viewBox = "0 0 24 24" > < path d = "M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54" / > < / svg >
< / a >
obikmer
< / label >
< ul class = "md-nav__list" data-md-scrollfix >
< li class = "md-nav__item" >
< a href = "../.." class = "md-nav__link" >
< span class = "md-ellipsis" >
Home
< / span >
< / a >
< / li >
< li class = "md-nav__item md-nav__item--nested" >
< input class = "md-nav__toggle md-toggle " type = "checkbox" id = "__nav_2" >
< label class = "md-nav__link" for = "__nav_2" id = "__nav_2_label" tabindex = "0" >
< span class = "md-ellipsis" >
Theory
< / span >
< span class = "md-nav__icon md-icon" > < / span >
< / label >
< nav class = "md-nav" data-md-level = "1" aria-labelledby = "__nav_2_label" aria-expanded = "false" >
< label class = "md-nav__title" for = "__nav_2" >
< span class = "md-nav__icon md-icon" > < / span >
Theory
< / label >
< ul class = "md-nav__list" data-md-scrollfix >
< li class = "md-nav__item" >
2026-04-29 22:52:42 +02:00
< a href = "../../kmers/" class = "md-nav__link" >
2026-04-16 22:38:20 +02:00
< span class = "md-ellipsis" >
Kmers and super-kmers
< / span >
< / a >
< / li >
< li class = "md-nav__item" >
< a href = "../../theory/encoding/" class = "md-nav__link" >
< span class = "md-ellipsis" >
DNA encoding
< / span >
< / a >
< / li >
< li class = "md-nav__item" >
< a href = "../../theory/entropy/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Entropy filter
< / span >
< / a >
< / li >
2026-04-29 22:52:42 +02:00
< li class = "md-nav__item" >
< a href = "../../theory/minimizer/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Minimizer selection
< / span >
< / a >
< / li >
2026-04-16 22:38:20 +02:00
< li class = "md-nav__item" >
< a href = "../../theory/indexing/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Partitioning architecture
< / span >
< / a >
< / li >
< / ul >
< / nav >
< / li >
< li class = "md-nav__item md-nav__item--active md-nav__item--nested" >
< input class = "md-nav__toggle md-toggle " type = "checkbox" id = "__nav_3" checked >
< label class = "md-nav__link" for = "__nav_3" id = "__nav_3_label" tabindex = "0" >
< span class = "md-ellipsis" >
Implementation
< / span >
< span class = "md-nav__icon md-icon" > < / span >
< / label >
< nav class = "md-nav" data-md-level = "1" aria-labelledby = "__nav_3_label" aria-expanded = "true" >
< label class = "md-nav__title" for = "__nav_3" >
< span class = "md-nav__icon md-icon" > < / span >
Implementation
< / label >
< ul class = "md-nav__list" data-md-scrollfix >
< li class = "md-nav__item" >
< a href = "../superkmer/" class = "md-nav__link" >
< span class = "md-ellipsis" >
SuperKmer
< / span >
< / a >
< / li >
< li class = "md-nav__item" >
< a href = "../kmer/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Kmer
< / span >
< / a >
< / li >
< li class = "md-nav__item" >
< a href = "../chunkreader/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Chunk reader
< / span >
< / a >
< / li >
< li class = "md-nav__item" >
< a href = "../pipeline/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Construction pipeline
< / span >
< / a >
< / li >
2026-04-29 22:52:42 +02:00
< li class = "md-nav__item" >
< a href = "../obipipeline/" class = "md-nav__link" >
< span class = "md-ellipsis" >
obipipeline library
< / span >
< / a >
< / li >
2026-04-16 22:38:20 +02:00
< li class = "md-nav__item" >
< a href = "../storage/" class = "md-nav__link" >
< span class = "md-ellipsis" >
On-disk storage
< / span >
< / a >
< / li >
< li class = "md-nav__item md-nav__item--active" >
< input class = "md-nav__toggle md-toggle" type = "checkbox" id = "__toc" >
< label class = "md-nav__link md-nav__link--active" for = "__toc" >
< span class = "md-ellipsis" >
MPHF selection
< / span >
< span class = "md-nav__icon md-icon" > < / span >
< / label >
< a href = "./" class = "md-nav__link md-nav__link--active" >
< span class = "md-ellipsis" >
MPHF selection
< / span >
< / a >
< nav class = "md-nav md-nav--secondary" aria-label = "Table of contents" >
< label class = "md-nav__title" for = "__toc" >
< span class = "md-nav__icon md-icon" > < / span >
Table of contents
< / label >
< ul class = "md-nav__list" data-md-component = "toc" data-md-scrollfix >
2026-04-29 22:52:42 +02:00
< li class = "md-nav__item" >
2026-05-17 10:20:22 +08:00
< a href = "#why-two-phases-are-needed" class = "md-nav__link" >
2026-04-29 22:52:42 +02:00
< span class = "md-ellipsis" >
2026-05-17 10:20:22 +08:00
Why two phases are needed
2026-04-29 22:52:42 +02:00
< / span >
< / a >
2026-05-17 10:20:22 +08:00
< nav class = "md-nav" aria-label = "Why two phases are needed" >
2026-04-29 22:52:42 +02:00
< ul class = "md-nav__list" >
< li class = "md-nav__item" >
2026-05-17 10:20:22 +08:00
< a href = "#phase-1-provisional-mphf-kmer-spectrum" class = "md-nav__link" >
2026-04-29 22:52:42 +02:00
< span class = "md-ellipsis" >
2026-05-17 10:20:22 +08:00
Phase 1 — provisional MPHF + kmer spectrum
2026-04-29 22:52:42 +02:00
< / span >
< / a >
< / li >
< li class = "md-nav__item" >
2026-05-17 10:20:22 +08:00
< a href = "#phase-2-definitive-mphf" class = "md-nav__link" >
2026-04-29 22:52:42 +02:00
< span class = "md-ellipsis" >
2026-05-17 10:20:22 +08:00
Phase 2 — definitive MPHF
2026-04-29 22:52:42 +02:00
< / span >
< / a >
< / li >
< / ul >
< / nav >
< / li >
2026-04-16 22:38:20 +02:00
< li class = "md-nav__item" >
2026-05-17 10:20:22 +08:00
< a href = "#mphf-candidates" class = "md-nav__link" >
2026-04-16 22:38:20 +02:00
< span class = "md-ellipsis" >
2026-05-17 10:20:22 +08:00
MPHF candidates
2026-04-16 22:38:20 +02:00
< / span >
< / a >
2026-04-29 22:52:42 +02:00
< / li >
< li class = "md-nav__item" >
< a href = "#mphf-choice-per-phase" class = "md-nav__link" >
< span class = "md-ellipsis" >
MPHF choice per phase
< / span >
< / a >
2026-04-16 22:38:20 +02:00
< / li >
< li class = "md-nav__item" >
< a href = "#space-at-scale" class = "md-nav__link" >
< span class = "md-ellipsis" >
Space at scale
< / span >
< / a >
< / li >
< li class = "md-nav__item" >
2026-05-17 10:20:22 +08:00
< a href = "#ptr_hash-configuration-phase-2" class = "md-nav__link" >
2026-04-16 22:38:20 +02:00
< span class = "md-ellipsis" >
2026-05-17 10:20:22 +08:00
ptr_hash configuration (phase 2)
2026-04-16 22:38:20 +02:00
< / span >
< / a >
2026-05-15 21:07:23 +08:00
< / li >
< li class = "md-nav__item" >
< a href = "#multilayer-index-architecture" class = "md-nav__link" >
< span class = "md-ellipsis" >
Multilayer index architecture
< / span >
< / a >
< nav class = "md-nav" aria-label = "Multilayer index architecture" >
< ul class = "md-nav__list" >
< li class = "md-nav__item" >
< a href = "#layer-structure" class = "md-nav__link" >
< span class = "md-ellipsis" >
Layer structure
< / span >
< / a >
< / li >
< li class = "md-nav__item" >
< a href = "#membership-verification" class = "md-nav__link" >
< span class = "md-ellipsis" >
Membership verification
< / span >
< / a >
< / li >
< li class = "md-nav__item" >
< a href = "#query-algorithm" class = "md-nav__link" >
< span class = "md-ellipsis" >
Query algorithm
< / span >
< / a >
< / li >
< li class = "md-nav__item" >
< a href = "#merging-layers" class = "md-nav__link" >
< span class = "md-ellipsis" >
Merging layers
< / span >
< / a >
< / li >
< / ul >
< / nav >
2026-04-16 22:38:20 +02:00
< / li >
< / ul >
< / nav >
< / li >
2026-04-29 22:52:42 +02:00
< li class = "md-nav__item" >
< a href = "../unitig_evidence/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Unitig evidence encoding
< / span >
< / a >
< / li >
2026-05-15 21:07:23 +08:00
< li class = "md-nav__item" >
< a href = "../obilayeredmap/" class = "md-nav__link" >
< span class = "md-ellipsis" >
obilayeredmap crate
< / span >
< / a >
< / li >
< li class = "md-nav__item" >
< a href = "../persistent_compact_int_vec/" class = "md-nav__link" >
< span class = "md-ellipsis" >
PersistentCompactIntVec
< / span >
< / a >
< / li >
< li class = "md-nav__item" >
< a href = "../persistent_bit_vec/" class = "md-nav__link" >
< span class = "md-ellipsis" >
PersistentBitVec
< / span >
< / a >
< / li >
2026-04-16 22:38:20 +02:00
< / ul >
< / nav >
< / li >
< li class = "md-nav__item md-nav__item--nested" >
< input class = "md-nav__toggle md-toggle " type = "checkbox" id = "__nav_4" >
< label class = "md-nav__link" for = "__nav_4" id = "__nav_4_label" tabindex = "0" >
< span class = "md-ellipsis" >
Architecture
< / span >
< span class = "md-nav__icon md-icon" > < / span >
< / label >
< nav class = "md-nav" data-md-level = "1" aria-labelledby = "__nav_4_label" aria-expanded = "false" >
< label class = "md-nav__title" for = "__nav_4" >
< span class = "md-nav__icon md-icon" > < / span >
Architecture
< / label >
< ul class = "md-nav__list" data-md-scrollfix >
< li class = "md-nav__item" >
< a href = "../../architecture/sequences/invariant/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Sequences
< / span >
< / a >
< / li >
2026-05-15 21:07:23 +08:00
< li class = "md-nav__item" >
< a href = "../../architecture/index_architecture/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Kmer index
< / span >
< / a >
< / li >
2026-04-16 22:38:20 +02:00
< / ul >
< / nav >
< / li >
< / ul >
< / nav >
< / div >
< / div >
< / div >
< div class = "md-sidebar md-sidebar--secondary" data-md-component = "sidebar" data-md-type = "toc" >
< div class = "md-sidebar__scrollwrap" >
< div class = "md-sidebar__inner" >
< nav class = "md-nav md-nav--secondary" aria-label = "Table of contents" >
< label class = "md-nav__title" for = "__toc" >
< span class = "md-nav__icon md-icon" > < / span >
Table of contents
< / label >
< ul class = "md-nav__list" data-md-component = "toc" data-md-scrollfix >
2026-04-29 22:52:42 +02:00
< li class = "md-nav__item" >
2026-05-17 10:20:22 +08:00
< a href = "#why-two-phases-are-needed" class = "md-nav__link" >
2026-04-29 22:52:42 +02:00
< span class = "md-ellipsis" >
2026-05-17 10:20:22 +08:00
Why two phases are needed
2026-04-29 22:52:42 +02:00
< / span >
< / a >
2026-05-17 10:20:22 +08:00
< nav class = "md-nav" aria-label = "Why two phases are needed" >
2026-04-29 22:52:42 +02:00
< ul class = "md-nav__list" >
< li class = "md-nav__item" >
2026-05-17 10:20:22 +08:00
< a href = "#phase-1-provisional-mphf-kmer-spectrum" class = "md-nav__link" >
2026-04-29 22:52:42 +02:00
< span class = "md-ellipsis" >
2026-05-17 10:20:22 +08:00
Phase 1 — provisional MPHF + kmer spectrum
2026-04-29 22:52:42 +02:00
< / span >
< / a >
< / li >
< li class = "md-nav__item" >
2026-05-17 10:20:22 +08:00
< a href = "#phase-2-definitive-mphf" class = "md-nav__link" >
2026-04-29 22:52:42 +02:00
< span class = "md-ellipsis" >
2026-05-17 10:20:22 +08:00
Phase 2 — definitive MPHF
2026-04-29 22:52:42 +02:00
< / span >
< / a >
< / li >
< / ul >
< / nav >
< / li >
2026-04-16 22:38:20 +02:00
< li class = "md-nav__item" >
2026-05-17 10:20:22 +08:00
< a href = "#mphf-candidates" class = "md-nav__link" >
2026-04-16 22:38:20 +02:00
< span class = "md-ellipsis" >
2026-05-17 10:20:22 +08:00
MPHF candidates
2026-04-16 22:38:20 +02:00
< / span >
< / a >
2026-04-29 22:52:42 +02:00
< / li >
< li class = "md-nav__item" >
< a href = "#mphf-choice-per-phase" class = "md-nav__link" >
< span class = "md-ellipsis" >
MPHF choice per phase
< / span >
< / a >
2026-04-16 22:38:20 +02:00
< / li >
< li class = "md-nav__item" >
< a href = "#space-at-scale" class = "md-nav__link" >
< span class = "md-ellipsis" >
Space at scale
< / span >
< / a >
< / li >
< li class = "md-nav__item" >
2026-05-17 10:20:22 +08:00
< a href = "#ptr_hash-configuration-phase-2" class = "md-nav__link" >
2026-04-16 22:38:20 +02:00
< span class = "md-ellipsis" >
2026-05-17 10:20:22 +08:00
ptr_hash configuration (phase 2)
2026-04-16 22:38:20 +02:00
< / span >
< / a >
2026-05-15 21:07:23 +08:00
< / li >
< li class = "md-nav__item" >
< a href = "#multilayer-index-architecture" class = "md-nav__link" >
< span class = "md-ellipsis" >
Multilayer index architecture
< / span >
< / a >
< nav class = "md-nav" aria-label = "Multilayer index architecture" >
< ul class = "md-nav__list" >
< li class = "md-nav__item" >
< a href = "#layer-structure" class = "md-nav__link" >
< span class = "md-ellipsis" >
Layer structure
< / span >
< / a >
< / li >
< li class = "md-nav__item" >
< a href = "#membership-verification" class = "md-nav__link" >
< span class = "md-ellipsis" >
Membership verification
< / span >
< / a >
< / li >
< li class = "md-nav__item" >
< a href = "#query-algorithm" class = "md-nav__link" >
< span class = "md-ellipsis" >
Query algorithm
< / span >
< / a >
< / li >
< li class = "md-nav__item" >
< a href = "#merging-layers" class = "md-nav__link" >
< span class = "md-ellipsis" >
Merging layers
< / span >
< / a >
< / li >
< / ul >
< / nav >
2026-04-16 22:38:20 +02:00
< / li >
< / ul >
< / nav >
< / div >
< / div >
< / div >
< div class = "md-content" data-md-component = "content" >
< article class = "md-content__inner md-typeset" >
2026-04-29 22:52:42 +02:00
< h1 id = "mphf-selection-two-phase-indexing-architecture" > MPHF selection — two-phase indexing architecture< / h1 >
2026-05-17 10:20:22 +08:00
< h2 id = "why-two-phases-are-needed" > Why two phases are needed< / h2 >
< p > Kmer indexing per partition proceeds in two phases. The separation is necessary because the exact number of surviving unique kmers is not known until after counting and filtering low-abundance kmers.< / p >
< h3 id = "phase-1-provisional-mphf-kmer-spectrum" > Phase 1 — provisional MPHF + kmer spectrum< / h3 >
< p > Implemented in < code > obikpartitionner::KmerPartition::count_kmer()< / code > .< / p >
< ol >
< li > < strong > Pass 1< / strong > : read the dereplicated superkmer file; enumerate all unique canonical kmers into a < code > HashSet< / code > . Exact count known after this pass.< / li >
< li > < strong > Build a provisional MPHF< / strong > (< code > GOFunction< / code > from the < code > ph< / code > crate) over the exact kmer set. Produces < code > mphf1.bin< / code > .< / li >
< li > < strong > Create < code > counts1.bin< / code > < / strong > : one zero-initialised < code > u32< / code > per MPHF slot (mmap'd).< / li >
< li > < strong > Pass 2< / strong > : re-read the dereplicated file; for each kmer, query < code > mphf1.get(kmer)< / code > and atomically accumulate the superkmer count into < code > counts1[slot]< / code > .< / li >
< li > < strong > Build kmer frequency spectrum< / strong > from < code > counts1< / code > : histogram < code > {count → n_kmers}< / code > , totals f0 (distinct kmers) and f1 (total abundance). Written to < code > kmer_spectrum_raw.json< / code > per partition, then merged globally.< / li >
< / ol >
< p > Files produced per partition:< / p >
< div class = "highlight" > < pre > < span > < / span > < code > part_XXXXX/
mphf1.bin — GOFunction (provisional MPHF, discarded after phase 2)
counts1.bin — [u32; n_kmers] kmer counts, mmap' d
kmer_spectrum_raw.json — local frequency spectrum
< / code > < / pre > < / div >
< h3 id = "phase-2-definitive-mphf" > Phase 2 — definitive MPHF< / h3 >
< p > After filtering (applying a min-count threshold derived from the spectrum) and building the local De Bruijn graph + unitigs (see < a href = "../pipeline/" > Construction pipeline< / a > ), the exact filtered kmer set is available via < code > unitigs.bin< / code > .< / p >
< p > < code > MphfLayer::build< / code > is called on the unitig file:< / p >
2026-04-29 22:52:42 +02:00
< ol >
2026-05-17 10:20:22 +08:00
< li > < strong > Pass 1< / strong > : iterate all canonical kmers from < code > unitigs.bin< / code > in parallel, build and store < code > mphf.bin< / code > (ptr_hash).< / li >
< li > < strong > Pass 2< / strong > : iterate sequentially, fill < code > evidence.bin< / code > , call the mode-specific < code > fill_slot< / code > callback.< / li >
2026-04-29 22:52:42 +02:00
< / ol >
2026-05-17 10:20:22 +08:00
< p > < code > mphf1.bin< / code > and < code > counts1.bin< / code > are no longer needed after phase 2 and can be deleted.< / p >
2026-04-29 22:52:42 +02:00
< hr / >
2026-05-17 10:20:22 +08:00
< h2 id = "mphf-candidates" > MPHF candidates< / h2 >
2026-04-16 22:38:20 +02:00
< p > < strong > boomphf< / strong > (BBHash algorithm, maintained by 10X Genomics):< / p >
< ul >
< li > ~3.7 bits/key; mature crate, used in production bioinformatics (Pufferfish, Piscem)< / li >
2026-05-17 10:20:22 +08:00
< li > Supports streaming construction (no exact count needed)< / li >
< li > Drawback: largest space footprint; streaming advantage is irrelevant at phase 2 since the exact count is available< / li >
2026-04-16 22:38:20 +02:00
< / ul >
< p > < strong > ptr_hash< / strong > (PtrHash algorithm, Groot Koerkamp, SEA 2025):< / p >
< ul >
2026-05-17 10:20:22 +08:00
< li > ~2.4 bits/key; fastest queries (≥2.1× – × < / li >
< li > Requires exact key count at construction — available at both phases after pass 1< / li >
< li > Published February 2025; accepted given performance profile and the fact that each MPHF is independently rebuildable from its unitig file< / li >
2026-04-16 22:38:20 +02:00
< / ul >
2026-05-17 10:20:22 +08:00
< p > < strong > FMPH/FMPHGO< / strong > (< code > ph< / code > crate, Beling, ACM JEA 2023):< / p >
2026-04-16 22:38:20 +02:00
< ul >
2026-05-17 10:20:22 +08:00
< li > ~2.1 bits/key — most compact; good query speed; deterministic construction< / li >
< li > Works well from an exact or slightly overestimated count< / li >
< li > < code > GOFunction< / code > (group-oriented variant) is the specific type used< / li >
2026-04-16 22:38:20 +02:00
< / ul >
2026-04-29 22:52:42 +02:00
< h2 id = "mphf-choice-per-phase" > MPHF choice per phase< / h2 >
2026-05-17 10:20:22 +08:00
< p > < strong > Phase 1< / strong > (provisional, discarded after spectrum computation): < code > ph::fmph::GOFunction< / code > . Compact, fast to build from the exact post-dedup kmer set. Query speed is secondary — the structure is only used during pass 2 of < code > count_kmer< / code > .< / p >
< p > < strong > Phase 2< / strong > (persistent, queried repeatedly): < strong > ptr_hash< / strong > . Exact key count is available from the unitig index; ptr_hash query speed (≥2.1× × < / p >
< p > boomphf is eliminated: largest space overhead, streaming advantage does not apply.< / p >
2026-04-29 22:52:42 +02:00
< hr / >
2026-04-16 22:38:20 +02:00
< h2 id = "space-at-scale" > Space at scale< / h2 >
2026-04-29 22:52:42 +02:00
< p > For 1 024 partitions × < / p >
2026-04-16 22:38:20 +02:00
< table >
< thead >
< tr >
< th > MPHF< / th >
< th > bits/key< / th >
< th > Total MPHF size< / th >
< / tr >
< / thead >
< tbody >
< tr >
< td > boomphf< / td >
< td > 3.7< / td >
< td > ~47 GB< / td >
< / tr >
< tr >
< td > ptr_hash< / td >
< td > 2.4< / td >
< td > ~31 GB< / td >
< / tr >
< tr >
2026-05-17 10:20:22 +08:00
< td > FMPH< / td >
2026-04-16 22:38:20 +02:00
< td > 2.1< / td >
< td > ~27 GB< / td >
< / tr >
< / tbody >
< / table >
2026-04-29 22:52:42 +02:00
< p > For a human genome at 30× – – < / p >
2026-05-17 10:20:22 +08:00
< hr / >
< h2 id = "ptr_hash-configuration-phase-2" > ptr_hash configuration (phase 2)< / h2 >
< div class = "highlight" > < pre > < span > < / span > < code > < span class = "k" > type< / span > < span class = "w" > < / span > < span class = "nc" > Mphf< / span > < span class = "w" > < / span > < span class = "o" > =< / span > < span class = "w" > < / span > < span class = "n" > PtrHash< / span > < span class = "o" > < < / span >
< span class = "w" > < / span > < span class = "kt" > u64< / span > < span class = "p" > ,< / span > < span class = "w" > < / span > < span class = "c1" > // key: canonical kmer raw encoding< / span >
< span class = "w" > < / span > < span class = "n" > CubicEps< / span > < span class = "p" > ,< / span > < span class = "w" > < / span > < span class = "c1" > // bucket fn: 2.4 bits/key, λ=3.5, α < / span >
< span class = "w" > < / span > < span class = "n" > CachelineEfVec< / span > < span class = "o" > < < / span > < span class = "nb" > Vec< / span > < span class = "o" > < < / span > < span class = "n" > CachelineEf< / span > < span class = "o" > > > < / span > < span class = "p" > ,< / span > < span class = "w" > < / span > < span class = "c1" > // remap: 11.6 bits/entry (Elias-Fano)< / span >
< span class = "w" > < / span > < span class = "n" > Xx64< / span > < span class = "p" > ,< / span > < span class = "w" > < / span > < span class = "c1" > // hasher: XXH3-64 with seed< / span >
< span class = "w" > < / span > < span class = "nb" > Vec< / span > < span class = "o" > < < / span > < span class = "kt" > u8< / span > < span class = "o" > > < / span > < span class = "p" > ,< / span > < span class = "w" > < / span > < span class = "c1" > // pilots< / span >
< span class = "o" > > < / span > < span class = "p" > ;< / span >
< / code > < / pre > < / div >
< p > < strong > Hasher — < code > Xx64< / code > < / strong > : canonical kmer raw values are left-aligned u64 with structural zeros in low bits (42 zeros for k=11, 2 zeros for k=31). < code > FxHash< / code > (single multiply) distributes these poorly; < code > Xx64< / code > (XXH3-64, seeded) handles structured input correctly.< / p >
< p > < strong > Bucket function — < code > CubicEps< / code > < / strong > : λ=3.5, α × < code > Linear/λ=3.0< / code > , 20% less space. < code > default_compact< / code > (λ=4.0) saves a further 12.5% at 2× < / p >
< p > < strong > Remap — < code > CachelineEfVec< / code > < / strong > : Elias-Fano variant packing 44 sorted 40-bit values per 64-byte cacheline (11.6 bits/value vs 32 for < code > Vec< u32> < / code > ). One cacheline per query; space win dominates at billion-scale key counts.< / p >
2026-05-15 21:07:23 +08:00
< hr / >
< h2 id = "multilayer-index-architecture" > Multilayer index architecture< / h2 >
< h3 id = "layer-structure" > Layer structure< / h3 >
2026-05-17 10:20:22 +08:00
< p > Each layer is a self-contained unit. See < a href = "../obilayeredmap/" > obilayeredmap< / a > for the full on-disk layout. The MPHF-relevant files are:< / p >
2026-05-15 21:07:23 +08:00
< div class = "highlight" > < pre > < span > < / span > < code > layer_i/
2026-05-17 10:20:22 +08:00
unitigs.bin — packed 2-bit nucleotide sequences (kmer evidence)
mphf.bin — ptr_hash phase-2 MPHF
evidence.bin — n ×
2026-05-15 21:07:23 +08:00
< / code > < / pre > < / div >
2026-05-17 10:20:22 +08:00
< p > Layers are < strong > disjoint< / strong > : a canonical kmer belongs to exactly one layer. Layer 0 is built from dataset A. Adding dataset B:< / p >
2026-05-15 21:07:23 +08:00
< ol >
2026-05-17 10:20:22 +08:00
< li > For each kmer in B: probe existing layers. If found, the kmer is already indexed.< / li >
< li > Collect kmers of B not present in any layer → set < code > B \ A< / code > .< / li >
< li > Build layer 1 from < code > B \ A< / code > (dereplicate → count → De Bruijn → unitigs → < code > MphfLayer::build< / code > ).< / li >
2026-05-15 21:07:23 +08:00
< / ol >
< h3 id = "membership-verification" > Membership verification< / h3 >
2026-05-17 10:20:22 +08:00
< p > ptr_hash maps any input to a valid slot — it does not natively detect absent keys. Membership is verified using the evidence entry: decode the kmer from < code > (chunk_id, rank)< / code > and compare to the query. A mismatch means the kmer is absent from this layer; probe the next layer.< / p >
2026-05-15 21:07:23 +08:00
< h3 id = "query-algorithm" > Query algorithm< / h3 >
2026-05-17 10:20:22 +08:00
< div class = "highlight" > < pre > < span > < / span > < code > fn query(kmer) → Option< (layer_index, slot)> :
for (i, layer) in layers.iter().enumerate():
slot = layer.mphf.index(kmer)
if layer.evidence.decode(slot) matches kmer:
return Some((i, slot))
2026-05-15 21:07:23 +08:00
return None
< / code > < / pre > < / div >
2026-05-17 10:20:22 +08:00
< p > Expected probe depth: 1 for kmers in layer 0. Each probe is a ptr_hash lookup (~10 ns) plus one evidence decode.< / p >
2026-05-15 21:07:23 +08:00
< h3 id = "merging-layers" > Merging layers< / h3 >
2026-05-17 10:20:22 +08:00
< p > Two layer chains can be merged by re-indexing their union through the full pipeline. This is expensive (full rebuild) but produces an optimal single-layer index. Merge is a maintenance operation, not a query-path requirement.< / p >
2026-04-16 22:38:20 +02:00
< / article >
< / div >
< script > var target = document . getElementById ( location . hash . slice ( 1 ) ) ; target && target . name && ( target . checked = target . name . startsWith ( "__tabbed_" ) ) < / script >
< / div >
< / main >
< footer class = "md-footer" >
< div class = "md-footer-meta md-typeset" >
< div class = "md-footer-meta__inner md-grid" >
< div class = "md-copyright" >
Made with
< a href = "https://squidfunk.github.io/mkdocs-material/" target = "_blank" rel = "noopener" >
Material for MkDocs
< / a >
< / div >
< / div >
< / div >
< / footer >
< / div >
< div class = "md-dialog" data-md-component = "dialog" >
< div class = "md-dialog__inner md-typeset" > < / div >
< / div >
< script id = "__config" type = "application/json" > { "annotate" : null , "base" : "../.." , "features" : [ ] , "search" : "../../assets/javascripts/workers/search.2c215733.min.js" , "tags" : null , "translations" : { "clipboard.copied" : "Copied to clipboard" , "clipboard.copy" : "Copy to clipboard" , "search.result.more.one" : "1 more on this page" , "search.result.more.other" : "# more on this page" , "search.result.none" : "No matching documents" , "search.result.one" : "1 matching document" , "search.result.other" : "# matching documents" , "search.result.placeholder" : "Type to start searching" , "search.result.term.missing" : "Missing" , "select.version" : "Select version" } , "version" : null } < / script >
< script src = "../../assets/javascripts/bundle.79ae519e.min.js" > < / script >
< script src = "https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js" > < / script >
< / body >
< / html >
